                         (<= start left)
                         (>= end left))))
         candidates (flatten (map (fn [[^Long begin ^Long finish]]
-                                   (.seek ^BGZFInputStream (.reader rdr) begin)
-                                   (read-to-finish rdr finish read-coordinate-alignment-block)) spans))]
+                                   (read-to-finish rdr begin finish read-coordinate-alignment-block)) spans))]
     (filter window candidates)))
 
 (defn load-headers

                  :deep read-alignment
                  :pointer pointer-read-alignment)
        candidates (flatten (map (fn [[^Long begin ^Long finish]]
                                   (.seek ^BGZFInputStream (.reader rdr) begin)
                                   (read-to-finish rdr finish read-fn)) spans))]
    (if (= deep-or-shallow :first-only)
      (read-alignments-first-only rdr spans window read-fn)
      (filter window candidates))))

  (loop [left-spans spans]
    (when-let [span (first left-spans)]
      (let [[^Long begin ^Long finish] span]
        (or
          (loop [left (read-to-finish rdr begin finish read-fn)]
            (when-let [one (first left)]
              (if (window one)
                [one]
